Tracing the origins of widespread highland species: a case of Neogene diversification across the Mexican sierras in an endemic lizard

An elevational shift facilitated the Mesoamerican diversification of Azure-hooded Jays (Cyanolyca cucullata) during the Great American Biotic Interchange

The Great American Biotic Interchange (GABI) was a key biogeographic event in the history of the Americas. The rising of the Panamanian land bridge ended the isolation of South America and ushered in a period of dispersal, mass extinction, and new community assemblages, which sparked competition, adaptation, and speciation. Diversification across many bird groups, and the elevational zonation of others, ties back to events triggered by the GABI. But the exact timing of these events is still being revealed, with recent studies suggesting a much earlier time window for faunal exchange, perhaps as early as 20 million years ago (Mya). Using a time-calibrated phylogenetic tree, we show that the jay genus Cyanolyca is emblematic of bird dispersal trends, with an early, pre-land bridge dispersal from Mesoamerica to South America 6.3-7.3 Mya, followed by a back-colonization of C. cucullata to Mesoamerica 2.3-4.8 Mya, likely after the land bridge was complete. As Cyanolyca species came into contact in Mesoamerica, they avoided competition due to a prior shift to lower elevation in the ancestor of C. cucullata. This shift allowed C. cucullata to integrate itself into the Mesoamerican highland avifauna, which our time-calibrated phylogeny suggests was already populated by higher-elevation, congeneric dwarf-jays (C. argentigula, C. pumilo, C. mirabilis, and C. nanus). The outcome of these events and fortuitous elevational zonation was that C. cucullata could continue colonizing new highland areas farther north during the Pleistocene. Resultingly, four C. cucullata lineages became isolated in allopatric, highland regions from Panama to Mexico, diverging in genetics, morphology, plumage, and vocalizations. At least two of these lineages are best described as species (C. mitrata and C. cucullata). Continued study will further document the influence of the GABI and help clarify how dispersal and vicariance shaped modern-day species assemblages in the Americas.

Forest cover and geographical distance influence fine-scale genetic structure of leaf-toed geckos in the tropical dry forests of western Mexico

The biodiversity within tropical dry forests (TDFs) is astounding and yet poorly catalogued due to inadequate sampling and the presence of cryptic species. In the Mexican TDF, endemic species are common, and the landscape has been continually altered by geological and anthropogenic changes. To understand how landscape and environmental variables have shaped the population structure of endemic species, we studied the recently described species of leaf-toed gecko, Phyllodactylus benedettii, in coastal western Mexico. Using double-digest restriction site-associated DNA sequencing data, we first explore population structure and estimate the number of ancestral populations. The results indicate a high degree of genetic structure with little admixture, and patterns corresponding to both latitudinal and altitudinal gradients. We find that genetic structure cannot be explained purely by geographical distance, and that ecological corridors may facilitate dispersal and gene flow. We then model the spatial distribution of P. benedettii in the TDF through time and find that the coastline has been climatically suitable for the species since the Last Glacial Maximum. Landscape genetic analyses suggest that the combination of isolation by distance (IBD) and isolation by resistance (IBR; forest cover) has influenced the spatial genetic structure of the species. Overall, our genomic data demonstrate fine-scale population structure in TDF habitat, a complex colonization history, and spatial patterns consistent with both IBD and other ecological factors. These results further highlight the Mexican TDF as a diversity hotspot and suggest that continued anthropogenic changes are likely to affect native fauna.

Phylogeography supports lineage divergence for an endemic rattlesnake (Crotalus ravus) of the Neotropical montane forest in the Trans-Mexican Volcanic Belt

The formation of the Trans-Mexican Volcanic Belt (TMVB) and Pleistocene climatic fluctuations have been shown to influence the diversification of lineages and species distributed throughout central Mexico. In some taxa, however, evidence of lineage diversification is not easily recognized, as often is the case in reptiles. Here we present a phylogeographic study on a Mexican endemic rattlesnake species (Crotalus ravus), with the aim of understanding how distinct lineages are distributed across the TMVB. Genetic (mtDNA) and genomic (ddRADseq) data were generated from samples across the species’ range to evaluate phylogeographic structure, estimate phylogenetic relationships and divergence times, and perform environmental niche modeling (ENM). Both datasets recover strong phylogeographic structuring of two distinct lineages on an east-west axis, with an estimated Pleistocene divergence (~1.47 Myr). The ENM suggest that the distribution of the two lineages experienced expansion and reduction events throughout recent evolutionary time. We attribute the diversification of C. ravus lineages to geological events associated with the formation of the TMVB, as well as Quaternary climate changes, both of which have been previously recognized in co-distributed taxa in the TMVB. This work emphasizes the existence of cryptic diversification processes in a morphologically conserved species distributed in a region of complex climatic and orogenic heterogeneity.

Phylogenomics of alligator lizards elucidate diversification patterns across the Mexican Transition Zone and support the recognition of a new genus

Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in Bayesian Phylogenetics and Phylogeography and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of north-eastern Mexico, and erected a new genus to better reflect evolutionary history. In summary, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbour substantial unrecognized diversity.

San Josecito Cave and Its Paleoecological Contributions for Quaternary Studies in Mexico

San Josecito Cave (2250 m elevation) is located nearby Aramberri, Nuevo León, northeastern Mexico, with excavations occurring in 1935–1941 and 1990. It is a paleontological cave and the significance of its faunal data rests in the understanding of the Quaternary ecosystems of the Mexican Plateau and the Southern Plains. This significance is underpinned by a consideration of associated stratigraphic and geochronological data. The fauna is composed of mollusks, amphibians, reptiles, birds, and mammals. More than 30 extinct vertebrate species have been identified, constituting one of the most important Quaternary localities in the Americas. Radiocarbon dates and faunal correlations indicate the excavated deposits represent an interval of time between 45,000 and 11,000 14C years BP. The current synthesis demonstrates that the previous view of the assemblage as a single local fauna is erroneous and that, instead, several successive local faunas are present within a stratigraphic framework. This finding underscores the need for detailed studies of single localities in building paleoenvironmental models. As a corollary, results point to the necessity of including all vertebrate classes represented from a locality in building those models. In addition, the field and analytical methodologies demonstrate the importance of very detailed paleontological excavations, with precise spatial and temporal controls, to assess the taphonomic history of a locality, construct a stratigraphic and geochronological framework, and infer the paleoecological conditions during the time span considered based on the number of local faunas represented. The recognition of San Josecito Cave as an important Late Pleistocene vertebrate paleontological locality is enhanced with the consideration of its faunal data for paleoenvironment reconstruction and possible contribution to Quaternary paleoclimatic modeling.

A new extinct species of alligator lizard (Squamata: Elgaria) and an expanded perspective on the osteology and phylogeny of Gerrhonotinae

BACKGROUND

Alligator lizards (Gerrhonotinae) are a well-known group of extant North American lizard. Although many fossils were previously referred to Gerrhonotinae, most of those fossils are isolated and fragmentary cranial elements that could not be placed in a precise phylogenetic context, and only a handful of known fossils are articulated skulls. The fossil record has provided limited information on the biogeography and phylogeny of Gerrhonotinae.

RESULTS

We redescribe a nearly complete articulated fossil skull from the Pliocene sediments of the Anza-Borrego Desert in southern California, and refer the specimen to the alligator lizard genus Elgaria. The fossil is a representative of a newly described species, Elgaria peludoverde. We created a morphological matrix to assess the phylogeny of alligator lizards and facilitate identifications of fossil gerrhonotines. The matrix contains a considerably expanded taxonomic sample relative to previous morphological studies of gerrhonotines, and we sampled two specimens for many species to partially account for intraspecific variation. Specimen-based phylogenetic analyses of our dataset using Bayesian inference and parsimony inferred that Elgaria peludoverde is part of crown Elgaria. The new species is potentially related to the extant species Elgaria kingii and Elgaria paucicarinata, but that relationship was not strongly supported, probably because of extensive variation among Elgaria. We explored several alternative biogeographic scenarios implied by the geographic and temporal occurrence of the new species and its potential phylogenetic placements.

CONCLUSIONS

Elgaria peludoverde is the first described extinct species of Elgaria and provides new information on the biogeographic history and diversification of Elgaria. Our research expands the understanding of phylogenetic relationships and biogeography of alligator lizards and strengthens the foundation of future investigations. The osteological data and phylogenetic matrix that we provided will be critical for future efforts to place fossil gerrhonotines. Despite limited intraspecific sampled sizes, we encountered substantial variation among gerrhonotines, demonstrating the value of exploring patterns of variation for morphological phylogenetics and for the phylogenetic placement of fossils. Future osteological investigations on the species we examined and on species we did not examine will continue to augment our knowledge of patterns of variation in alligator lizards and aid in phylogenetics and fossil placement.

Phylogenomics, floral evolution, and biogeography of Lithospermum L. (Boraginaceae)

Lithospermum (Boraginaceae), a geographically cosmopolitan medium-sized genus, includes diverse floral morphology, with variation in corolla size and shape and in breeding system. Over the past decade, multiple studies have examined the evolutionary history of Lithospermum, with most utilizing DNA regions from the plastid genome and/or the nuclear ribosomal internal transcribed spacer. These studies have, in general, not resulted in well-resolved and well-supported phylogenies. In the present study, 298 nuclear DNA regions, amplified via target sequence capture, were utilized for phylogenetic reconstruction for Lithospermum and relatives in Boraginaceae, and patterns of floral evolution, species diversification, and biogeography were examined. Based on multiple phylogenetic methods, Lithospermum is resolved as monophyletic, and the New World species of the genus are also monophyletic. While minimal phylogenetic incongruence is resolved within the nuclear genome, incongruence between the nuclear and plastid genomes is recovered. This is likely due to incomplete lineage sorting during early diversification of the genus in the Americas approximately 7.8 million years ago. At least four shifts to longer corollas are identified throughout Lithospermum, and this may be due to selection for hummingbird-pollinated flowers, particularly for species in Mexico and the southwestern United States. In the New World, one clade of species of the genus diversified primarily across the United States and Canada, and another radiated throughout the mountains of Mexico.

High genetic diversity and stable Pleistocene distributional ranges in the widespread Mexican red oak Quercus castanea Née (1801) (Fagaceae)

The Mexican highlands are areas of high biological complexity where taxa of Nearctic and Neotropical origin and different population histories are found. To gain a more detailed view of the evolution of the biota in these regions, it is necessary to evaluate the effects of historical tectonic and climate events on species. Here, we analyzed the phylogeographic structure, historical demographic processes, and the contemporary period, Last Glacial Maximum (LGM) and Last Interglacial (LIG) ecological niche models of Quercus castanea, to infer the historical population dynamics of this oak distributed in the Mexican highlands. A total of 36 populations of Q. castanea were genotyped with seven chloroplast microsatellite loci in four recognized biogeographic provinces of Mexico: the Sierra Madre Occidental (western mountain range), the Central Plateau, the Trans-Mexican Volcanic Belt (TMVB, mountain range crossing central Mexico from west to east) and the Sierra Madre del Sur (SMS, southern mountain range). We obtained standard statistics of genetic diversity and structure and tested for signals of historical demographic expansions. A total of 90 haplotypes were identified, and 29 of these haplotypes were restricted to single populations. The within-population genetic diversity was high (mean h S = 0.72), and among-population genetic differentiation showed a strong phylogeographic structure (N ST = 0.630 > G ST = 0.266; p < .001). Signals of demographic expansion were identified in the TMVB and the SMS. The ecological niche models suggested a considerable percentage of stable distribution area for the species during the LGM and connectivity between the TMVB and the SMS. High genetic diversity, strong phylogeographic structure, and ecological niche models suggest in situ permanence of Q. castanea populations with large effective population sizes. The complex geological and climatic histories of the TMVB help to explain the origin and maintenance of a large proportion of the genetic diversity in this oak species.

Potential distribution and habitat connectivity of Crotalus triseriatus in Central Mexico

The dusky rattlesnake, Crotalustriseriatus, used to be very abundant in many parts of the highlands of central Mexico, but with the increasing human population and associated activities, the rattlesnake habitats and populations have suffered drastic reductions and fragmentation. At the moment, the most important habitat features, associated with the presence of C.triseriatus, the current potential distribution and the landscape connectivity amongst the populations of the State of Mexico and Mexico City, are unknown. Therefore, we used the maximum entropy modelling software (MAXENT) to analyse the current potential distribution and most important habitat features, associated with the presence of the species. The variables with the highest contribution to the model were: proportion of Abies forest, minimum temperature of coldest month, maximum temperature of the warmest month, proportion of Pinus forest and annual precipitation. Furthermore, we found connectivity corridors only within mountain chains. Our results highlight the necessity for conserving the patches of Abies forest and preserving the populations of C.triseriatus and the connectivity of the landscape.

Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa

Local adaptation is a critical evolutionary process that allows plants to grow better in their local compared to non-native habitat and results in species-wide geographic patterns of adaptive genetic variation. For forest tree species with a long generation time, this spatial genetic heterogeneity can shape the ability of trees to respond to rapid climate change. Here, we identify genomic variation that may confer local environmental adaptations and then predict the extent of adaptive mismatch under future climate as a tool for forest restoration or management of the widely distributed high-elevation oak species Quercus rugosa in Mexico. Using genotyping by sequencing, we identified 5,354 single nucleotide polymorphisms (SNPs) genotyped from 103 individuals across 17 sites in the Trans-Mexican Volcanic Belt, and, after controlling for neutral genetic structure, we detected 74 F ST outlier SNPs and 97 SNPs associated with climate variation. Then, we deployed a nonlinear multivariate model, Gradient Forests, to map turnover in allele frequencies along environmental gradients and predict areas most sensitive to climate change. We found that spatial patterns of genetic variation were most strongly associated with precipitation seasonality and geographic distance. We identified regions of contemporary genetic and climatic similarities and predicted regions where future populations of Q. rugosa might be at risk due to high expected rate of climate change. Our findings provide preliminary details for future management strategies of Q. rugosa in Mexico and also illustrate how a landscape genomic approach can provide a useful tool for conservation and resource management strategies.

Late Pleistocene genetic diversification and demographic expansion in the widely distributed neotropical ant Neoponera villosa (Ponerinae)

Phylogeographic studies of continent-wide distributed species are key to understand population dynamics processes that occurred at large geographical scales. Here, we examined two mitochondrial (mt) DNA sequence (COI, Cyt b) and eight nuclear microsatellites markers to investigate the cohesiveness, genetic diversity and demographic history of Neoponera villosa (Fabricius), a ponerine ant species widely distributed along most part of the Neotropics and southern Nearctic. The reconstructed phylogeny and mt variation supported the cohesiveness of the examined populations of N. villosa. The species probably originated in South America during the late Pliocene/middle Pleistocene and subsequently dispersed to Central America and the Transitional Nearctic-Neotropical zone during the late Pleistocene, with an increase in its population size ca. 30 thousand years ago. The limited phylogeographic structure observed in N. villosa supports its late Pleistocene range expansion and gene flow among distant geographic areas in central and southern Mexico and Central America.

Potential distribution of the endemic imbricate alligator lizard (Barisia imbricata imbricata) in highlands of central Mexico

Barisia imbricata imbricata is an endemic anguid lizard living in the highlands of central Mexico, mainly in the Trans-Mexican Volcanic Belt, but its current distribution is not well defined. For this reason, it is critical to make a systematic study in order to determine the potential distribution of this subspecies. We considered 13 environmental and anthropogenic variables recognized to be important to determine the presence of B. i. imbricata; we also used eight presence-only modeling methods and selected three to generate an ensemble model. The Maxent algorithm was used to obtain the most important variables. The variables with highest contribution to the model were: maximum temperature of the warmest month, altitude, Abies forest and Pinus forest. From the estimated potential distribution (9614.1 km2), 8053.4 km2 (83.8%) are located in the Trans-Mexican Volcanic Belt, 3821.4 km2 (39.7%) are located in natural protected areas and 2418.2 km2 (25.2%) are in crop fields. The whole potential distribution is highly fragmented and characterized by the presence of human activities, which could have long-term consequences, increasing extinction risk.

Genetic diversity and genetic structure of an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified agricultural landscape: implications for conservation

It is necessary to determine genetic diversity of fragmented populations in highly modified landscapes to understand how populations respond to land-use change. This information will help guide future conservation and management strategies. We conducted a population genetic study on an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified landscape near the Toluca metropolitan area, in order to provide crucial information for the conservation of this species. There was medium levels of genetic diversity, with a few alleles and genotypes. We identified three genetically differentiated clusters, likely as a result of different habitat cover type. We also found evidence of an ancestral genetic bottleneck and medium values of effective population size. Inbreeding coefficients were low and there was a moderate gene flow. Our results can be used as a basis for future research and C. triseriatus conservation efforts, particularly considering that the Trans-Mexican Volcanic Belt is heavily impacted by destructive land-use practices.

Population Structure in the Roundtail Chub (Gila robusta Complex) of the Gila River Basin as Determined by Microsatellites: Evolutionary and Conservation Implications

Ten microsatellite loci were characterized for 34 locations from roundtail chub (Gila robusta complex) to better resolve patterns of genetic variation among local populations in the lower Colorado River basin. This group has had a complex taxonomic history and previous molecular analyses failed to identify species diagnostic molecular markers. Our results supported previous molecular studies based on allozymes and DNA sequences, which found that most genetic variance was explained by differences among local populations. Samples from most localities were so divergent species-level diagnostic markers were not found. Some geographic samples were discordant with current taxonomy due to admixture or misidentification; therefore, additional morphological studies are necessary. Differences in spatial genetic structure were consistent with differences in connectivity of stream habitats, with the typically mainstem species, G. robusta, exhibiting greater genetic connectedness within the Gila River drainage. No species exhibited strong isolation by distance over the entire stream network, but the two species typically found in headwaters, G. nigra and G. intermedia, exhibited greater than expected genetic similarity between geographically proximate populations, and usually clustered with individuals from the same geographic location and/or sub-basin. These results highlight the significance of microevolutionary processes and importance of maintaining local populations to maximize evolutionary potential for this complex. Augmentation stocking as a conservation management strategy should only occur under extreme circumstances, and potential source populations should be geographically proximate stocks of the same species, especially for the headwater forms.

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.

Late Miocene lineage divergence and ecological differentiation of rare endemic Juniperus blancoi: clues for the diversification of North American conifers

Western North America and Mexico contain a large number of conifer species. This diversity could be the product of orographic and climate changes of the late Tertiary and Quaternary. In this study, we focus on the evolutionary history of Juniperus blancoi, in order to determine the impact of climate change and environmental heterogeneity on population differentiation. We estimated the population structure, phylogenetic relationships and historical demography of J. blancoi populations using nuclear genes. We correlated genetic structure with ecological differentiation, divergence times and changes in population size. Populations of J. blancoi are differentiated into three lineages that correspond to low-, mid- and high-altitude populations. The three groups diversified in the late Miocene, early Pliocene, with only a few events of gene flow since then. Two lineages in the north exhibited a pattern of population growth during the Pleistocene that could be linked to climate changes. Populations of J. blancoi experienced significant ecological differentiation and early divergence events, which correspond to periods of global cooling and mountain uplift during the Miocene. This suggests that mountain ranges in tropical and subtropical latitudes play an important role in the speciation and persistence of conifer taxa in diversity hotspots, by providing diverse environmental conditions.

Ecological speciation in Nolina parviflora (Asparagaceae): lacking spatial connectivity along of the Trans-Mexican Volcanic Belt

The hypothesis of ecological speciation states that as populations diverge in different niches, reproductive isolation evolves as a by-product of adaptation to these different environments. In this context, we used Nolina parviflora as a model to test if this species evolved via ecological speciation and to explore current and historical gene flow among its populations. Nolina parviflora is a montane species endemic to Mexico with its geographical distribution restricted largely to the Trans-Mexican Volcanic Belt. This mountain range is one of the most complex geological regions in Mexico, having undergone volcanism from the mid-Miocene to the present. Ecologically, the Trans-Mexican Volcanic Belt possesses different types of vegetation, including tropical dry forest; oak, pine, pine-oak, and pine-juniper forests; and xerophytic scrub--all of which maintain populations of N. parviflora. Using species distribution models, climatic analyses, spatial connectivity and morphological comparisons, we found significant differences in climatic and morphological variables between populations of N. parviflora in two distinct Trans-Mexican Volcanic Belt regions (east vs. west). This could mean that the geographically isolated populations diverged from one another via niche divergence, indicating ecological speciation. Spatial connectivity analysis revealed no connectivity between these regions under the present or last glacial maximum climate models, indicating a lack of gene flow between the populations of the two regions. The results imply that these populations may encompass more than a single species.

Tracking climate change in a dispersal-limited species: reduced spatial and genetic connectivity in a montane salamander

Tropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane-adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically, we used ecological niche modelling (ENM) and measured spatial connectivity and gene flow (using both mtDNA and microsatellite markers) across extant populations of P. leprosa in the Trans-Mexican Volcanic Belt (TVB). Our results indicate significant spatial and genetic isolation among populations, but we cannot distinguish between isolation by distance over time or current landscape barriers as mechanisms shaping population genetic divergences. Combining ecological niche modelling, spatial connectivity analyses, and historical and contemporary genetic signatures from different classes of genetic markers allows for inference of historical evolutionary processes and predictions of the impacts future climate change will have on the genetic diversity of montane taxa with low dispersal rates. Pseudoeurycea leprosa is one montane species among many endemic to this region and thus is a case study for the continued persistence of spatially and genetically isolated populations in the highly biodiverse TVB of central Mexico.